The Larger the Better: Analysis of a Scalable Spectral Clustering Algorithm with Cosine Similarity

Chen (2018) proposed a scalable spectral clustering algorithm for cosine similarity to handle the task of clustering large data sets. It runs extremely fast, with a linear complexity in the size of the data, and achieves state of the art accuracy. This paper conducts perturbation analysis of the algorithm to understand the effect of discarding a perturbation term in an eigendecomposition step. Our results show that the accuracy of the approximation by the scalable algorithm depends on the connectivity of the clusters, their separation and sizes, and is especially accurate for large data sets.

Signaling pathway perturbation analysis for assessment of biological impact of cigarette smoke on lung cells

Exposure to cigarette smoke (CS) results in injury to the epithelial cells of the human respiratory tract and has been implicated as a causative factor in the development of chronic obstructive pulmonary disease and lung cancers. The application of omics-scale methodologies has improved the capacity to understand cellular signaling processes underlying response to CS exposure. We report here the development of an algorithm based on quantitative assessment of transcriptomic profiles and signaling pathway perturbation analysis (SPPA) of human bronchial epithelial cells (HBEC) exposed to the toxic components present in CS. HBEC were exposed to CS of different compositions and for different durations using an ISO3308 smoking regime and the impact of exposure was monitored in 2263 signaling pathways in the cell to generate a total effect score that reflects the quantitative degree of impact of external stimuli on the cells. These findings support the conclusion that the SPPA algorithm provides an objective, systematic, sensitive means to evaluate the biological impact of exposures to CS of different compositions making a powerful comparative tool for commercial product evaluation and potentially for other known or potentially toxic environmental smoke substances.